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E39 (1997 - 2003) The BMW 5-Series (E39 chassis) was introduced in the United States as a 1997 model year car and lasted until the 2004 when the E60 chassis was released. The United States saw several variations including the 525i, 528i, 530i and 540i. -- View the E39 Wiki

I can't open my tailgate or the window without having to do it manually by pulling on the cord inside the hatch.

Everytime i try to open it, it will unlock and move the tailage to where you have to open it manually, but then it will re-engage the actuator and lock again. Also, when i put the car in reverse, it will do the same thing.

I've trying pulling on the tailgate while unlocking it, but it won't disengage fully, and it will re-lock again.

Could this be a wiring issue in the hatch? I wonder this because my rear wiper and washer hasn't worked since owning the car, and i've taken a quick look to see that some wires are either on their way out or already broken in the upper part of the hatch.

...Maybe the wagon has the same issues? One way to find out is to visually check.

It does...and I'd definitely check once you can get the tail gate open. If memory is correct...I think you can open just the glass lift gate...look to the far right and you should see a loom that goes into the roof of the car. You may have to remove some of the small cover pieces on the right hinge to access the loom.